Job ID = 1294424 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T22:36:52 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-02T22:37:58 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-02T22:37:58 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-02T22:37:58 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-02T22:37:58 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 23,008,083 reads read : 23,008,083 reads written : 23,008,083 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:38 23008083 reads; of these: 23008083 (100.00%) were unpaired; of these: 1291578 (5.61%) aligned 0 times 14514880 (63.09%) aligned exactly 1 time 7201625 (31.30%) aligned >1 times 94.39% overall alignment rate Time searching: 00:10:38 Overall time: 00:10:38 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3391213 / 21716505 = 0.1562 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 03 Jun 2019 08:05:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287595/SRX287595.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287595/SRX287595.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287595/SRX287595.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287595/SRX287595.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 03 Jun 2019 08:05:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:05:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:05:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287595/SRX287595.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287595/SRX287595.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287595/SRX287595.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287595/SRX287595.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 03 Jun 2019 08:05:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:05:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:05:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287595/SRX287595.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287595/SRX287595.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287595/SRX287595.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287595/SRX287595.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 03 Jun 2019 08:05:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:05:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:05:16: 1000000 INFO @ Mon, 03 Jun 2019 08:05:17: 1000000 INFO @ Mon, 03 Jun 2019 08:05:18: 1000000 INFO @ Mon, 03 Jun 2019 08:05:22: 2000000 INFO @ Mon, 03 Jun 2019 08:05:24: 2000000 INFO @ Mon, 03 Jun 2019 08:05:25: 2000000 INFO @ Mon, 03 Jun 2019 08:05:29: 3000000 INFO @ Mon, 03 Jun 2019 08:05:31: 3000000 INFO @ Mon, 03 Jun 2019 08:05:33: 3000000 INFO @ Mon, 03 Jun 2019 08:05:35: 4000000 INFO @ Mon, 03 Jun 2019 08:05:38: 4000000 INFO @ Mon, 03 Jun 2019 08:05:41: 4000000 INFO @ Mon, 03 Jun 2019 08:05:42: 5000000 INFO @ Mon, 03 Jun 2019 08:05:44: 5000000 INFO @ Mon, 03 Jun 2019 08:05:48: 6000000 INFO @ Mon, 03 Jun 2019 08:05:49: 5000000 INFO @ Mon, 03 Jun 2019 08:05:51: 6000000 INFO @ Mon, 03 Jun 2019 08:05:54: 7000000 INFO @ Mon, 03 Jun 2019 08:05:57: 6000000 INFO @ Mon, 03 Jun 2019 08:05:58: 7000000 INFO @ Mon, 03 Jun 2019 08:06:01: 8000000 INFO @ Mon, 03 Jun 2019 08:06:05: 7000000 INFO @ Mon, 03 Jun 2019 08:06:05: 8000000 INFO @ Mon, 03 Jun 2019 08:06:07: 9000000 INFO @ Mon, 03 Jun 2019 08:06:12: 9000000 INFO @ Mon, 03 Jun 2019 08:06:12: 8000000 INFO @ Mon, 03 Jun 2019 08:06:14: 10000000 INFO @ Mon, 03 Jun 2019 08:06:19: 10000000 INFO @ Mon, 03 Jun 2019 08:06:20: 9000000 INFO @ Mon, 03 Jun 2019 08:06:20: 11000000 INFO @ Mon, 03 Jun 2019 08:06:26: 11000000 INFO @ Mon, 03 Jun 2019 08:06:27: 12000000 INFO @ Mon, 03 Jun 2019 08:06:28: 10000000 INFO @ Mon, 03 Jun 2019 08:06:33: 12000000 INFO @ Mon, 03 Jun 2019 08:06:33: 13000000 INFO @ Mon, 03 Jun 2019 08:06:35: 11000000 INFO @ Mon, 03 Jun 2019 08:06:39: 14000000 INFO @ Mon, 03 Jun 2019 08:06:39: 13000000 INFO @ Mon, 03 Jun 2019 08:06:43: 12000000 INFO @ Mon, 03 Jun 2019 08:06:46: 15000000 INFO @ Mon, 03 Jun 2019 08:06:46: 14000000 INFO @ Mon, 03 Jun 2019 08:06:52: 13000000 INFO @ Mon, 03 Jun 2019 08:06:52: 16000000 INFO @ Mon, 03 Jun 2019 08:06:53: 15000000 INFO @ Mon, 03 Jun 2019 08:06:59: 17000000 INFO @ Mon, 03 Jun 2019 08:07:00: 16000000 INFO @ Mon, 03 Jun 2019 08:07:00: 14000000 INFO @ Mon, 03 Jun 2019 08:07:05: 18000000 INFO @ Mon, 03 Jun 2019 08:07:07: 17000000 INFO @ Mon, 03 Jun 2019 08:07:07: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:07:07: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:07:07: #1 total tags in treatment: 18325292 INFO @ Mon, 03 Jun 2019 08:07:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:07:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 08:07:08: #1 tags after filtering in treatment: 18325292 INFO @ Mon, 03 Jun 2019 08:07:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:07:08: #1 finished! INFO @ Mon, 03 Jun 2019 08:07:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:07:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:07:08: 15000000 INFO @ Mon, 03 Jun 2019 08:07:09: #2 number of paired peaks: 153 WARNING @ Mon, 03 Jun 2019 08:07:09: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Mon, 03 Jun 2019 08:07:09: start model_add_line... INFO @ Mon, 03 Jun 2019 08:07:09: start X-correlation... INFO @ Mon, 03 Jun 2019 08:07:09: end of X-cor INFO @ Mon, 03 Jun 2019 08:07:09: #2 finished! INFO @ Mon, 03 Jun 2019 08:07:09: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 08:07:09: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 03 Jun 2019 08:07:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287595/SRX287595.10_model.r WARNING @ Mon, 03 Jun 2019 08:07:09: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:07:09: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 03 Jun 2019 08:07:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 08:07:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:07:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:07:13: 18000000 INFO @ Mon, 03 Jun 2019 08:07:16: 16000000 INFO @ Mon, 03 Jun 2019 08:07:16: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:07:16: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:07:16: #1 total tags in treatment: 18325292 INFO @ Mon, 03 Jun 2019 08:07:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:07:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 08:07:16: #1 tags after filtering in treatment: 18325292 INFO @ Mon, 03 Jun 2019 08:07:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:07:16: #1 finished! INFO @ Mon, 03 Jun 2019 08:07:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:07:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:07:18: #2 number of paired peaks: 153 WARNING @ Mon, 03 Jun 2019 08:07:18: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Mon, 03 Jun 2019 08:07:18: start model_add_line... INFO @ Mon, 03 Jun 2019 08:07:18: start X-correlation... INFO @ Mon, 03 Jun 2019 08:07:18: end of X-cor INFO @ Mon, 03 Jun 2019 08:07:18: #2 finished! INFO @ Mon, 03 Jun 2019 08:07:18: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 08:07:18: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 03 Jun 2019 08:07:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287595/SRX287595.05_model.r WARNING @ Mon, 03 Jun 2019 08:07:18: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:07:18: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 03 Jun 2019 08:07:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 08:07:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:07:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:07:23: 17000000 INFO @ Mon, 03 Jun 2019 08:07:31: 18000000 INFO @ Mon, 03 Jun 2019 08:07:34: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:07:34: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:07:34: #1 total tags in treatment: 18325292 INFO @ Mon, 03 Jun 2019 08:07:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:07:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 08:07:34: #1 tags after filtering in treatment: 18325292 INFO @ Mon, 03 Jun 2019 08:07:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:07:34: #1 finished! INFO @ Mon, 03 Jun 2019 08:07:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:07:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:07:35: #2 number of paired peaks: 153 WARNING @ Mon, 03 Jun 2019 08:07:35: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Mon, 03 Jun 2019 08:07:35: start model_add_line... INFO @ Mon, 03 Jun 2019 08:07:36: start X-correlation... INFO @ Mon, 03 Jun 2019 08:07:36: end of X-cor INFO @ Mon, 03 Jun 2019 08:07:36: #2 finished! INFO @ Mon, 03 Jun 2019 08:07:36: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 08:07:36: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 03 Jun 2019 08:07:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287595/SRX287595.20_model.r WARNING @ Mon, 03 Jun 2019 08:07:36: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:07:36: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 03 Jun 2019 08:07:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 08:07:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:07:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:07:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:08:05: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:08:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287595/SRX287595.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:08:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287595/SRX287595.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:08:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287595/SRX287595.10_summits.bed INFO @ Mon, 03 Jun 2019 08:08:19: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1783 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:08:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:08:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287595/SRX287595.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:08:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287595/SRX287595.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:08:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287595/SRX287595.05_summits.bed INFO @ Mon, 03 Jun 2019 08:08:27: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2165 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:08:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287595/SRX287595.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:08:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287595/SRX287595.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:08:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287595/SRX287595.20_summits.bed INFO @ Mon, 03 Jun 2019 08:08:45: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1332 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。